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Annotation of /pkg/ChangeLog

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Revision 599 - (view) (download)

1 : bates 599 2005-03-03 Douglas Bates <bates@bates1-home>
2 :    
3 :     * src/lmer.c (lmer_fitted): Added.
4 :    
5 : bates 596 2005-03-02 Douglas Bates <bates@bates1-home>
6 :    
7 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
8 :    
9 : bates 582 2005-02-28 Douglas Bates <bates@bates1-home>
10 :    
11 :     * src/*.c,po/,inst/po: Internationalization and localization of
12 :     the package.
13 :    
14 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
15 :     R_ldl.c file.
16 :    
17 :     * src/flame.[ch]: Removed these source files.
18 :    
19 :     * src/dtrMatrix.c (make_array_triangular): Move to Mutils
20 :    
21 :     * src/LU.[ch],src/init.c: absorb in factorizations
22 :    
23 :     * src/Mutils.h: prepare for internationalization
24 :    
25 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
26 :     this file
27 :    
28 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
29 :    
30 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
31 :    
32 :     * R/dtrMatrix.R: fix t() method
33 :    
34 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
35 :     * NAMESPACE: export them (and import generics from "methods")
36 :     * tests/group-methods.R : and test them.
37 :    
38 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
39 :     border case
40 :    
41 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
42 :    
43 :     * DESCRIPTION (Version): 0.95-2 released to CRAN
44 :    
45 :     * src/dgBCMatrix.c:
46 :     * src/lmer.c: many changes
47 :     * ...
48 :    
49 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
50 :    
51 :     * R/Matrix.R: add more sophisticated show() method.
52 :    
53 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
54 :    
55 :     * */* : almost complete reorganization of classes.
56 :    
57 : bates 460 2005-01-26 Douglas Bates <bates@bates7>
58 :    
59 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
60 :     for the geMatrix class.
61 :    
62 :     2005-01-24 Douglas Bates <bates@bates7>
63 :    
64 :     * src/Makefile (clean): Remove *.a and *.so
65 :    
66 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
67 :    
68 :     2005-01-23 Douglas Bates <bates@bates7>
69 :    
70 :     * src/lmer.c (Lind): Definition of Lind was backwards. This only
71 :     had an effect in cases with more than 2 grouping factors.
72 :    
73 : bates 415 2005-01-03 Douglas Bates <bates@bates1-home>
74 :    
75 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
76 :    
77 : bates 410 2004-12-23 Douglas Bates <bates@bates1-home>
78 :    
79 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
80 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
81 :    
82 : bates 392 2004-12-14 Douglas Bates <bates@bates1-home>
83 :    
84 :     * R/sscMatrix.R: Add determinant methods
85 :    
86 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
87 :     for tripletMatrix to matrix.
88 :    
89 : bates 388 2004-12-13 Douglas Bates <bates@bates1-home>
90 :    
91 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
92 :     no longer used.
93 :    
94 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
95 :     with dynamic allocation of scratch arrays.
96 :    
97 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
98 :     for multivariate random effects with multiple grouping factors.
99 :     Fixes part but not all of #15.
100 :    
101 : bates 375 2004-12-03 Douglas Bates <bates@bates1-home>
102 :    
103 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
104 :     scalar grouping factors corrected.
105 :    
106 :     2004-11-29 Douglas Bates <bates@bates1-home>
107 :    
108 :     * src/bCrosstab.c: remove diag_update which is no longer used
109 :    
110 : bates 350 2004-11-16 Douglas Bates <bates@bates1-home>
111 :    
112 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
113 :     .h file can be included.
114 :    
115 : bates 342 2004-11-12 Douglas Bates <bates@bates1-home>
116 :    
117 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
118 : bates 342 Complete allocation of slots in NEW_OBJECT.
119 :    
120 :     * src/Mutils.h: Moved list of symbols to an include file
121 :    
122 :     2004-11-11 Douglas Bates <bates@bates1-home>
123 :    
124 :     * src/geMutils.c (Matrix_init): remove unused function
125 :    
126 :     2004-11-10 Douglas Bates <bates@bates1-home>
127 :    
128 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
129 :    
130 : bates 327 2004-11-05 Douglas Bates <bates@bates1-home>
131 :    
132 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
133 :    
134 : bates 303 2004-10-27 Douglas Bates <bates@bates1-home>
135 :    
136 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
137 :    
138 : bates 296 2004-10-04 Douglas Bates <bates@bates1-home>
139 :    
140 :     * src/init.c: Created R_init_Matrix and added registration of C
141 :     routines.
142 :    
143 : bates 283 2004-10-02 Douglas Bates <bates@bates1-home>
144 :    
145 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
146 :    
147 : bates 229 2004-06-15 Douglas Bates <bates@bates7>
148 :    
149 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
150 :    
151 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
152 :    
153 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
154 :    
155 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
156 :    
157 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
158 :     ssclme_update_mm
159 :    
160 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
161 :    
162 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
163 :     in the order of unconstrained and constrained parameters.
164 :     (ssclme_gradient): Added the gradients (not yet correct for
165 :     multidimensional, unconstrained case).
166 :    
167 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
168 :    
169 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
170 :    
171 :     * src/Makefile.win: Remove unneeded ranlib call
172 :    
173 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
174 :    
175 :     * DESCRIPTION (Version): New release
176 :    
177 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
178 :    
179 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
180 :    
181 :     * src/triplet_to_col.c: Create triplet_to_col as a native
182 :     function, not the version from umfpack. There were problems with
183 :     the configuration of UMFPACK for 64-bit processors and there was
184 :     only one umfpack routine being used so I moved it here.
185 :    
186 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
187 :    
188 :     * src/ssclme.c (ssclme_variances): New function.
189 :    
190 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
191 :    
192 :     * src/ssclme.c (ssclme_fitted): Added function.
193 :    
194 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
195 :    
196 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
197 :     store the dimnames in the XtX and bVar slots
198 :     (ssclme_update_mm): Change the dimensions of the bVar slot
199 :     components and the returned value from ssclme_ranef.
200 :    
201 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
202 :    
203 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
204 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
205 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
206 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
207 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
208 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
209 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
210 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
211 :     Moved the pdMat classes from the lme4 package.
212 :    
213 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
214 :    
215 :     * man/ssclme-class.Rd: Update definition and documentation of the
216 :     ssclme class to include the DIsqrt slot.
217 :    
218 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
219 :     (much faster using dsyrk, a level 3 BLAS routine).
220 :    
221 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
222 :    
223 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
224 :    
225 :     * tests/ssclme.R: Modify the test to account for the permutation
226 :     of the levels of the grouping factors.
227 :    
228 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
229 :    
230 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
231 :     directly into the ssclme class definition.
232 :    
233 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
234 :    
235 :     * DESCRIPTION (Date): New release
236 :    
237 :     * man/ssclme-class.Rd: new file.
238 :    
239 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
240 :     works and it's fast!
241 :    
242 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
243 :    
244 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
245 :    
246 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
247 :    
248 :     * DESCRIPTION (Date): New release
249 :    
250 :     * NAMESPACE: Don't export ssclme.
251 :    
252 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
253 :     school data.
254 :    
255 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
256 :    
257 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
258 :     keep track of the fixed-effects and the response. Counts also
259 :     gets an extra element, which is always one.
260 :    
261 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
262 :    
263 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
264 :    
265 :     * src/cscMatrix.c (csc_transpose): new function
266 :    
267 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
268 :     (csc_components_transpose): new function
269 :    
270 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
271 :    
272 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
273 :     triplets
274 :    
275 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
276 :    
277 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
278 :    
279 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
280 :     and all other .h files in src.
281 :    
282 :     * src/Makefile.win: This and other Makefile.win files contributed
283 :     by Brian Ripley.
284 :    
285 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
286 :    
287 :     * R/syMatrix.R: Added methods for "%*%".
288 :    
289 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
290 :     poMatrix object.
291 :    
292 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
293 :    
294 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
295 :    
296 :     2004-01-25 Douglas Bates <bates@bates2_home>
297 :    
298 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
299 :    
300 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
301 :     of nrow.
302 :    
303 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
304 :    
305 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
306 :     subdirectories.
307 :    
308 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
309 :    
310 :     * src/taucs.h: Accidently referred to global header files
311 :     instead of local files.
312 :    
313 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
314 :    
315 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
316 :     and methods and replaced all classes with S4 classes.
317 :    
318 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
319 :    
320 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
321 :    
322 :     * src/R_LapackPP.cc: Change method of calculating determinants
323 :    
324 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
325 :    
326 :     * DESCRIPTION (Version): removed empty data directory as requested
327 :     by CRAN maintainers. Changed version number and date.
328 :    
329 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
330 :    
331 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
332 :     under Windows.
333 :    
334 :     * Added configure.win and src/Makevars.win as requested by Brian
335 :     Ripley.
336 :    
337 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
338 :    
339 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
340 :     Hornik.
341 :    
342 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
343 :    
344 :     * configure.ac: Replaced configure.in with configure.ac
345 :     contributed by Kurt Hornik.
346 :    
347 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
348 :     version for R-1.5.0
349 :    
350 : maechler 512
351 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
352 :    
353 :     * man/eigen.Rd: Removed the .Alias in the example

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